Application of parsimony analysis of endemicity in Amazonian biogeography: an example with primates

The distributions of 51 non-human primate species are used for Parsimony Analysis of Endemicity (PAE) to determine the relationships among 14 interfluvial regions in the Amazon basin, South America. Two most parsimonious cladograms were found. The strict consensus tree of these cladograms suggests an early separation between Lower Amazonia (eastern) and Upper Amazonia (western). The major clusters of interfluvial regions identified in the PAE cladogram are congruent with the areas of endemism delimited for birds. When interfluvial regions are converted into avian areas of endemism, the PAE cladogram is congruent with one of the two general areas cladograms suggested for Amazonia based on phylogenies of several clades of forest birds. Our analysis suggests that PAE can be used as a tool to objectively identify areas of endemism at an intra-continental scale as well as to make historical inferences. However, the value of a PAE cladogram in this latter application should be always evaluated by congruence with area cladograms built upon cladistic biogeography procedures.     

Humoral response to oligomeric human immunodeficiency virus type 1 envelope protein.

The humoral immune response to human immunodeficiency virus type 1 (HIV-1) is often studied by using monomeric or denatured envelope proteins (Env). However, native HIV-1 Env complexes that maintain quaternary structure elicit immune responses that are qualitatively distinct from those seen with monomeric or denatured Env. To more accurately assess the levels and types of antibodies elicited by HIV-1 infection, we developed an antigen capture enzyme-linked immunosorbent assay using a soluble, oligomeric form of HIV-1IIIB Env (gp140) that contains gp120 and the gp41 ectodomain. The gp140, captured by various monoclonal antibodies (MAbs), retained its native oligomeric structure: it bound CD4 and was recognized by MAbs to conformational epitopes in gp120 and gp41, including oligomer-specific epitopes in gp41. We compared the reactivities of clade B and clade E serum samples to captured Env preparations and found that while both reacted equally well with oligomeric gp140, clade B seras reacted more strongly with monomeric gp120 than did clade E samples. However, these differences were minimized when gp120 was captured by a V3 loop MAb, which may lead to increased exposure of the CD4 binding site. We also measured the ability of serum samples to block binding of MAbs to epitopes in gp120 and gp41. Clade B serum samples consistently blocked binding of oligomer-dependent MAbs to gp41 and, to a slightly lesser extent, MAbs to the CD4 binding site in gp120. Clade E serum samples showed equivalent or greater blocking of oligomer-dependent gp41 antibodies and considerably less blocking of CD4-binding-site MAbs. Finally, we found that < 5% of the antibodies in clade B sera bound to epitopes present only in monomeric gp120, 30% bound to epitopes present in both monomeric gp120 and oligomeric gp140, and 70% bound to epitopes present in oligomeric gp140, which includes gp41. Thus, captured oligomeric Env closely reflects the antigenic characteristics of Env protein on the surface of virions and infected cells, retains highly conserved epitopes that are recognized by antibodies raised against different clades, and makes it possible to detect a much greater fraction of total anti-HIV-1 Env activity in sera than does native monomeric gp120.     

Polymorphism and Ultrastructure of a Colpodean Ciliate of the Genus Platyophryides Foissner, 1987

ABSTRACT. A ciliate isolated from a pond in Brazil, transformed to a giant form when its food was shifted from a bacterial prey to a ciliate prey. This polymorphism is immediately reversible when the prey ciliates, either Tetrahymena or Colpidium , disappear from the culture medium. By its life cycle, morphology, and ultrastructure, this ciliate belongs to the Class Colpodea. it could belong to the genus Platyophryides Foissner, 1987, except that its micronucleus is not enveloped by the macronuclear membrane. The systematic position of the genus Platyophryides , the validity of the three species in this genus, and the characteristics of the Cyrtolophosidida are discussed.     

Brain Synthesis and Cerebrovascular Action of Epoxygenase Metabolites of Arachidonic Acid

The purpose of this study was to determine if whole brain makes epoxygenase metabolites of arachidonic acid and, if so, whether they are vasoactive on the cerebral microcirculation. Blood-free mouse brain slices were incubated with exogenous radiolabeled arachidonic acid, and the extracted metabolites were resolved by HPLC. Metabolite structures were confirmed by gas chromatography/mass spectrometry. In addition to prostaglandins, leukotriene B4, and hydroxyeicosatetraenoic acids, mouse brain metabolized arachidonic acid into several other compounds. Among them, we identified 5,6- and 14,15-epoxyeicosatrienoic acid. Next, we tested the effect of topical application of brain-synthesized 5,6-epoxyeicosatrienoic acid and synthetic epoxyeicosatrienoic acids on in vivo rabbit cerebral arteriolar diameter using the cranial window technique and in vivo microscopy. Brain-synthesized 5,6-epoxyeicosatrienoic acid caused a transient 28% arteriolar dilation, similar to that produced by 5 micrograms/ml of synthetic 5,6-epoxyeicosatrienoic acid. A concentration of synthetic 14,15- and 11,12-epoxyeicosatrienoic acid of 5 micrograms/ml CSF had little or no effect on diameter, whereas 8,9-epoxyeicosatrienoic acid caused a maximum dilation of 8%. These studies suggest that brain-synthesized 5,6-epoxyeicosatrienoic acid may play a role in the normal or pathophysiological regulation of the cerebral microcirculation.     

On the origin and colonization of house mice in the Madeira Islands

The skulls and skins of adult house mice from the Madeira Islands have been studied and compared with those from the Salvage Islands and with material from the neighbouring Portuguese mainland man-associated and wild forms, respectively Mus musclus domesticus Rutty, 1772 and M. sprelus Lataste, 1883. Differences between island and mainland populations were found in some of the analysed features. Insular skins of mice were found to be smaller than those of specimens from the mainland. However, in Madeiran and Salvage mice the toothrows were much more developed than in the mainland house mice. It is considered that the causes of these differences lie in the different characteristics of the habitats, mainly food availability, and also in the isolation of populations. Mus musculus domesticus appears to be the only form of the house mouse to have so far successfully colonized the Madeiras.     

Role of the SH3-Ligand Domain of Simian Immunodeficiency Virus Nef in Interaction with Nef-Associated Kinase and Simian AIDS in Rhesus Macaques

The nef gene of the human and simian immunodeficiency viruses (HIV and SIV) is dispensable for viral replication in T-cell lines; however, it is essential for high virus loads and progression to simian AIDS (SAIDS) in SIV-infected adult rhesus macaques. Nef proteins from HIV type 1 (HIV-1), HIV-2, and SIV contain a proline-Xaa-Xaa-proline (PxxP) motif. The region of Nef with this motif is similar to the Src homology region 3 (SH3) ligand domain found in many cell signaling proteins. In virus-infected lymphoid cells, Nef interacts with a cellular serine/threonine kinase, designated Nef-associated kinase (NAK). In this study, analysis of viral clones containing point mutations in the nef gene of the pathogenic clone SIVmac239 revealed that several strictly conserved residues in the PxxP region were essential for Nef-NAK interaction. The results of this analysis of Nef mutations in in vitro kinase assays indicated that the PxxP region in SIV Nef was strikingly similar to the consensus sequence for SH3 ligand domains possessing the minus orientation. To test the significance of the PxxP motif of Nef for viral pathogenesis, each proline was mutated to an alanine to produce the viral clone SIVmac239-P¹⁰⁴A/P¹⁰⁷A. This clone, expressing Nef that does not associate with NAK, was inoculated into seven juvenile rhesus macaques. In vitro kinase assays were performed on virus recovered from each animal; the ability of Nef to associate with NAK was restored in five of these animals as early as 8 weeks after infection. Analysis of nef genes from these viruses revealed patterns of genotypic reversion in the mutated PxxP motif. These revertant genotypes, which included a second-site suppressor mutation, restored the ability of Nef to interact with NAK. Additionally, the proportion of revertant viruses increased progressively during the course of infection in these animals, and two of these animals developed fatal SAIDS. Taken together, these results demonstrated that in vivo selection for the ability of SIV Nef to associate with NAK was correlated with the induction of SAIDS. Accordingly, these studies implicate a role for the conserved SH3 ligand domain for Nef function in virally induced immunodeficiency.